Readseq

Service Retirement

We remind you that it is not long until the EBI's Wise2DBA and Promoterwise services are retired on 15th April 2018. Alternatives can be found at Exonerate, BWA or BLAT. If you have any concerns, please contact us via support.

Readseq

Introduction

Readseq reads and converts biosequences between a selection of common biological sequence formats, including EMBL, GenBank and fasta sequence formats.

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

The first steps are usually where the user sets the tool input (e.g. sequences, databases...)

In the following steps, the user has the possibility to change the default tool parameters

And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Input Sequences

Input Sequence

One or more sequences to be translated can be entered directly into this form. Sequences can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is a 2MB limit.

Sequence File Upload

A file containing one or more valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be uploaded and used as input for the translation. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters. There is a 2MB limit.

Step 2 - Select parameters

Input Format

Input format name

Format Name

Value

Auto-detected

0

EMBL

4

GenBank

2

Fasta(Pearson)

8

Clustal/ALN

22

ACEDB

25

BLAST

20

DNAStrider

6

FlatFeat/FFF

23

GCG

5

GFF

24

IG/Stanford

1

MSF

15

NBRF

3

PAUP/NEXUS

17

Phylip(Phylip4)

12

Phylip3.2

11

PIR/CODATA

14

Plain/Raw

13

SCF

21

XML

19

Default value is: Auto-detected [0]

Output Format

Output format name.

Format Name

Value

EMBL

4

GenBank

2

Fasta(Pearson)

8

Clustal/ALN

22

ACEDB

25

DNAStrider

6

FlatFeat/FFF

23

GCG

5

GFF

24

IG/Stanford

1

MSF

15

NBRF

3

PAUP/NEXUS

17

Phylip(Phylip4)

12

Phylip3.2

11

PIR/CODATA

14

Plain/Raw

13

Pretty

18

XML

19

Default value is: EMBL [4]

Output Case

Change alphabet case for output sequences.

Default value is: No change [none]

Remove Gap Symbols

Remove gap symbols for output sequences.

label

value

None

none

Symbol -

-

Symbol .

.

Default value is: None [none]

Reverse-Complement of Input Sequencess

Reverse-complement of input sequences

Default value is: no [false]

Translate Symbols

Translate input symbol to output symbol.

Default value is:

Feature Selection

Feature to select

Feature

Description

attenuator

C_region

CAAT_signal

CDS

conflict

D-loop

D_segment

enhancer

exon

GC_signal

gene

iDNA

intron

J_segment

LTR

mat_peptide

misc_binding

misc_difference

misc_feature

misc_recomb

misc_RNA

misc_signal

misc_structure

modified_base

mRNA

N_region

old_sequence

polyA_signal

polyA_site

precursor_RNA

prim_transcript

primer_bind

promoter

protein_bind

RBS

repeat_region

repeat_unit

rep_origin

rRNA

S_region

satellite

scRNA

sig_peptide

snRNA

source

stem_loop

STS

TATA_signal

terminator

transit_peptide

tRNA

unsure

V_region

V_segment

variation

3'clip

3'UTR

5'clip

5'UTR

-10_signal

-35_signal

-

Feature Handle

Handling selectd features - to remove or extract sequence of selected features.

label

value

None

none

Remove sequence of selected features

remove

Extract sequence of selected features

extract

Default value is: None [none]

Subrange

Subrange of sequence feature locations to extract. E.g., -1000..0 -- 1000 bases upstream to start of feature; 1..end1 -- the full range of the feature; end1..end100 -- from the end to 100 bases downstream of the feature; -100..end100 -- 100 bases upstream to 100 bases downstream; join-100..10,end1..end100 -- 100 bases upstream to 10 into joined with the end to 100 bases downstream.

Default value is:

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).